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Acute myeloid leukemia (AML) is a hematopoietic cell disorder characterized by a block in differentiation and increased proliferation and survival of malignant blasts. Expansion of the malignant cell clone effects the normal production of blood cells and – if left untreated – leads to death. Receptor tyrosine kinases (RTKs) play an important role in the pathogenesis of AML, as they are either often mutated or overexpressed. In normal hematopoiesis, RTK signal termination is tightly controlled, and involves ubiquitination, internalization, endocytosis and degradation. Cbl proteins are E3 ligases and have been shown to ubiquitinate several activated RTKs, including Flt3 and Kit, targeting them for degradation. Recently, several Cbl mutations have been identified: Cbl-R420Q was identified in an AML patient and Cbl-70Z was identified in a mouse lymphoma model. In this thesis work, the role of these Cbl mutants in Kit signaling and in a mouse transplantation model was studied. Cbl mutants (Cbl-R420Q, Cbl-70Z) have the ability to transform the myeloid 32D cell line in cooperation with Kit WT. Cbl mutants along with Kit promoted interleukin-3 (IL3)-independent proliferation and enhanced the cell survival of 32D cells. In contrast, expression of the Cbl mutants alone did not confer IL3-independent growth. Stem cell factor (SCF, the Kit ligand) dependent growth was enhanced in the presence of Cbl mutants and Cbl mutants promoted colonogenic growth in the presence of Kit. Furthermore, Cbl mutants inhibited the ubiquitination of the activated Kit receptor. In addition, Cbl mutants inhibited the endocytosis of the activated Kit receptor. Retroviral expression of Cbl mutants in transplanted bone marrow induced a generalized mastocytosis, a myeloproliferative disease and, in rare care cases, myeloid leukemia. Splenomegaly was observed in the presence of Cbl mutants. Furthermore, mast cells with variable range of infiltration were noticed in all the vital organs (spleen, liver, bone marrow, lung, kidney, heart) of Cbl (mutant) transplanted mice. Almost all recipients of bone marrow cells transduced with Cbl mutants developed a lethal hematologic disorder with a mean latency of 341 days in the Cbl-R420Q group and 395 days in the Cbl-70Z group. This is the first published report on a hematological disease with Cbl mutants in a mouse model. Co-immunoprecipitation studies indicated that Cbl-70Z binds to Kit, even in the absence of Kit ligand. Cbl-R420Q also bound to Kit in the absence of SCF, albeit to a lesser extent. Association of Cbl mutants to Kit was enhanced in the presence of SCF. Signaling studies demonstrated the constitutive activation of Akt and Erk in the presence of Cbl mutants and Kit. In addition, Cbl mutants enhanced the SCF-dependent Kit, Akt and Erk activation. Cbl-70Z, in association with kinase-dead Kit (Kit-KD) or kinase-dead Flt3 (Flt3-KD), conferred IL3-independent growth and survival to the myeloid 32D cell line. Cbl-R420Q provided only a slight growth advantage in the presence of Kit-KD. As demonstrated by pharmacological inhibition studies, Akt activation was necessary for the transformation mediated by Cbl-70Z and Kit-KD / Flt3-KD. Cbl mutants enhanced the Src family kinases (SFKs) activity. The pharmacological inhibition of SFK activity inhibited the proliferation and colonogenic growth. Interaction was found between Cbl-70Z, SFKs and Kit-KD. The SFK member Fyn was identified to bind to Cbl. In addition, kinase activity of SFKs was necessary for binding to Cbl, since SFKs inhibition by PP-2 abolished the binding between the complex-binding partners. Dasatinib and PP-2, both SFK inhibitors, inhibited the Cbl and Akt phosphorylation indicating that Fyn acts upstream of Akt. Inhibition of Kit with imatinib reduced the proliferation of cells overexpressing Kit WT and Cbl-70Z much stronger compared with cells expressing Kit-KD and Cbl-70Z, but much less than the dual KIT/SFK inhibitor dasatinib. This indicated that Kit kinase activity was required but not essential. The data presented in this thesis work implies that both RTK and SFK inhibition may have to be targeted, in order to effectively prevent transformation. In summary, the present thesis work indicates an important role of Cbl, Kit and SFKs in myeloid transformation and deregulated signal transduction.
This thesis demonstrates the advancement of PELDOR spectroscopy beyond its original design of distance measurements in order to disentangle a maximum amount of information additionally encoded in the PELDOR data. In particular, the successful synthesis of novel polynitroxide radicals is described as well as the extraction of the relative orientation of spin labels, conformational flexibility and the separation of dipolar and exchange coupling via orientation selective PELDOR measurements in combination with PESIM based simulations. Moreover, the method of PELDOR "Spin Counting" was experimentally validated.
The transporter associated with antigen processing-like (TAPL) acts as a lysosomal ATP-dependent polypeptide transporter with broad length selectivity. To characterize in detail its substrate specificity, a procedure for solubilization, purification and functional reconstitution of human TAPL was developed. TAPL was expressed in Sf9 insect cells with the baculovirus expression system and solubilized from crude membranes. By intensive screening of detergents, the mild non-ionic detergents digitonin and dodecylmaltoside were found to be ideal for solubilization with respect to efficiency, long term stability, and functionality of TAPL. TAPL was isolated in a two-step procedure with a yield of 500 micro g/L cell culture and, subsequently, reconstituted into proteoliposomes. The KM(pep) for the peptide RRYCfKSTEL (f refers to fluorescence label) and KM(ATP) were determined to be 10.5 ± 2.3 micro M and 97.6 ± 27.5 micro M, respectively, which are in the same range as the Michaelis-Menten constants determined in the membranes. The peptide transport activity of the reconstituted TAPL strongly depends on the lipid composition. Interestingly, the E. coli lipids are prefered over other tested natural lipids extracts. Moreover, phosphatidylcholine, the most abundant phospholipid in eukaryotic cells influenced TAPL activity in a dose dependent manner. In addition, some negatively charged lipids like DOPA and DOPS increased peptide transport activity with preference for DOPS. However, DOPE or egg PG which are also negatively charged had no effect. It seems not only the charge but also the specific head group of phospholipids that has impact on the function of TAPL. With the help of combinatorial peptide libraries containing D-amino acid residues at defined positions as well as bulky fluorescein labeled peptides, the key positions of the peptides were localized to the N- and C-terminal residues with respect to peptide transport. The C-terminal position has the strongest selectivity since modification at this position shows strongest impact on peptide transport. Additionally, positions 2 and 3 of the peptide also have weak influence on peptide selectivity. Subsequently, the residue preferences at the key positions were systematically investigated by combinatorial peptide libraries with defined residues at certain positions. At both ends, TAPL favors positively charged, aromatic, or hydrophobic residues and disfavors negatively charged residues as well as asparagine and methionine. The residue preferences at the key positions are valid for peptide substrates with different length, indicating a general rule for TAPL selectivity. Besides specific interactions of both terminal residues, electrostatic interactions are important, since peptides with positive net charge are more efficiently transported than negatively charged ones. By size exclusion chromatography (SEC) and blue native PAGE, TAPL purified in the presence of digitonin or dodecylmaltoside had an apparent molecular weight of 200 kDa which is close to the theoretical molecular mass of the TAPL homodimer (172 kDa). The purified and reconstituted TAPL showed specific ATP hydrolysis activity which can be inhibited by orthovanadate. TAPL in proteoliposomes showed 6-fold higher ATP hydrolysis than digitonin solubilized protein, indicating the phospholipids impact on TAPL function. However, no peptide substrate stimulated ATPase activity was observed. For site-specific labeling of TAPL, eight cysteines in each half transporter were replaced by alanine or valine. The TAPL cys-less mutant showed the same peptide transport activity as TAPL wt. Based on the functional TAPL cys-less mutant, seven single cysteine mutants were introduced into strategic positions. All single cysteine mutants in the TMD did not influence peptide transport, whereas the mutant L701C, which is close to the conserved H-loop motif, displayed impaired transport. TAPL orthologs Haf-4 and Haf-9 from Caenorhabditis elegans possess around 40% sequence identities with TAPL and 50% with each other. Both proteins are putative half transporters and reported to be involved in the intestinal granule formation (Bauer, 2006; Kawai et al., 2009). To further understand the physiological functions of these two proteins, they were expressed in Sf9 insect cells. Haf-4 and Haf-9 showed weak but specific ATP- and peptide-dependent peptide transport activity for the given peptide RRYCfKSTEL. Therefore, it was proposed that the physiological roles for Haf-4 and Haf-9 might be related to their peptide transport activity. Besides forming functional homodimeric complex as estimated by the peptide transport activities, both half transporter could also form heteromers which was confirmed by coimmunoprecipitation. However, the heteromers showed decreased transport activity.
5-lipoxygenase (5-LO) is the key enzyme in the formation of inflammatory leukotrienes, which are mediators of inflammation and allergy. The 5-LO catalyses the oxidation of arachidonic acid to 5-HPETE and subsequently to LTA4. The leukotrienes are involved in the development and maintenance of inflammatory diseases, like asthma and allergic rhinitis. Additionally, 5-LO is overexpressed in some cancer types, although its relevance is still not fully understood. 5-LO expressing cells are B- lymphocytes and cells of myeloid origin like monocytes, macrophages and granulocytes. The 5-LO promoter lacks a TATA or CCAT box and covers two CpG islands. These are characteristics of a housekeeping gene, but as the 5-LO is not expressed ubiquitiously, the expression of the 5-LO is tightly regulated. Epigenetic mechanisms were known to be involved in the control of the 5-LO expression. The HDAC inhibitor TsA significantly induced the transcriptional activity of the 5-LO promoter in reporter gene assays as well as on 5-LO mRNA transcript level in MM6 cells. The GC-boxes GC4 and GC5 in the proximal 5-LO promoter were identified to be essential for the TsA effect, as deletion of these element led to an attenuated TsA effect in reporter gene assay. Recruitment of the transcription factors Sp1 and Sp3 and the RNA polymerase II to the 5-LO promoter was detectable after TsA treatment in MM6 cells by chromatin immunoprecipitation assays (ChIP), while the acetylation status of histone H4 remained unchanged. Likewise it is known that DNA methylation leads to silencing of 5-LO expression in-vitro and in-vivo. The 5-LO promoter is densely methylated in the cell line U937, but unmethylated in HL-60 cells and - elucidated in this study - also in MM6 cells. Reporter gene assays with in-vitro methylated 5-LO promoter containing plasmids revealed that the frequency of methylated CpGs is directly proportional to reduction of 5-LO promoter activity. Incubation of U937 cells with 5-AdC, an inhibitor of DNA methyltransferases, was able to reactivate 5-LO transcription and to demethylate CpG dinucleotides. In the first part of this study the mechanism of TsA induced promoter activation was further investigated. I elucidated the mechanism of Sp1 and Sp3 recruitment to the 5-LO promoter after TsA treatment. Immnoprecipitation assay was used to detect a transcription factor complex containing Sp1 or Sp3 interacting with HDAC proteins, which might change its composition after TsA treatment. Besides the posttranslational modifications of the transcription factors Sp1 and Sp3 after TsA treatment were investigated, potentially causing an increased interaction of the proteins with the 5-LO promoter. Both aspects and their response in HDAC inhibition have been described. TsA did not affect the composition of the Sp1/HDAC1/HDAC2 complex. Sp3 was not located in a complex with the HDAC enzymes. Acetylation of Sp1 and Sp3 was detectable, but no change occurred after TsA treatment. Since neither release of the transcription factors off a complex, nor alterations in posttranslational modifications of Sp1 and Sp3 are the reason for the increased Sp1 and Sp3 binding to the 5-LO promoter, I elucidated alterations in the chromatin structure. The acetylation status of the histone proteins H3 and H4, as well as the chromatin marks H3K4me3, representing active chromatin, and H3K9me, representative for repressive state, were investigated. Additionally, the time course of the TsA effect was determined on 5-LO mRNA level using real-time PCR. The acetylation status of the histone proteins on the 5-LO core promoter correlated with the basal 5-LO mRNA transcript expression in MM6, HL-60 and U937 cells. The highest 5-LO mRNA level was detectable in MM6 cells, followed by HL-60 cells. The lowest 5-LO mRNA level was detected in 5-LO promoter methylated U937 cells. The order of the basal 5-LO mRNA expression of the three cell lines correlates with the basal acetylation status of histone proteins H3 and H4. In MM6 cells the highest basal levels in acH3 and acH4 were detected, followed by HL-60 and U937 cells. Moreover, the data obtained in U937 cells revealed that the correlation between DNA methylation and histone hypoacetylation is alike on the 5-LO promoter. TsA treatment induced the 5-LO mRNA level in the three cell lines with different intensity: 5-LO mRNA level in MM6 cells was induced 11-fold, in HL-60 cells 6- fold and in U937 cells 4- fold. The histone acetylation and methylation levels on the 5-LO promoter after TsA incubation were investigated. No increase in acH3 and acH4, but in H3K4me3 was detectable in MM6 cells by ChIP assay. HL-60 cells showed an increase in acH3 and acH4 as well as in H3K4me3. H3K9me was only detectable in untreated U937 cells, but disappeared after TsA treatment, while acH3, acH4 and H3K4me3 increased constantly after TsA treatme nt. A strong correlation between the histone modifications and the time course of the mRNA expression was detectable in all three cell lines. The combination of the posttranslational modifications acH3, acH4 and H3K4me3 led to a fast effect in transcriptional activation and the maxima of acH3 and acH4 were usually associated with the maximum in 5-LO mRNA transcript level. An increase in H3K4me3 alone, as detected in MM6 cells, led to continuous increase in the 5-LO mRNA expression with a late maximum. Additionally, we detected a slight overall decrease in 5-LO promoter methylation in U937 cells after TsA treatment. This fact taken together with the observed histone modifications could explain the 4- fold response in 5-LO mRNA level to TsA treatment of the methylated cell line U937. Another aim of the present study was to identify the specific HDAC enzymes involved in the 5-LO promoter regulation. Reporter gene assays and real-time PCR with selective HDAC inhibitors revealed that HDACs of class I are involved in 5-LO promoter regulation, namely HDAC 1, 2 and 3. The influence of each of the enzymes seemed to depend on the cell type, as inhibition of HDACs 2, 3 strongly induced 5-LO promoter activity in reporter gene assay in HeLa cells, whereas in MM6 cells HDACs 1 and 2, 3 seemed to be responsible for the 5-LO promoter regulation, measured as 5-LO mRNA level. The HDACs of class IIa and class III are not involved in the regulation of 5-LO mRNA expression. The second part of this study investigated the influence of MBD proteins on the methylated 5-LO promoter and the 5-LO mRNA expression. ChIP assays revealed MBD1, 2 and MeCP2 protein binding to the proximal 5-LO promoter in U937 cells. MBD1 was detectable on the 5-LO promoter in unmethylated HL-60 cells, while no MBD protein was located on the 5-LO promoter in MM6 cells. To elucidate the functional role of the MBD proteins, stable knocked down of MBD proteins was established in U937 cells. 5-LO mRNA transcript level was determined in the knock down clones by real-time PCR. The 5-LO transcript level was increased in all knock down samples. MBD2 knock down clones showed the highest effect in activating 5-LO with a 3- and 4.4-fold increase in the 5-LO mRNA level, followed by MBD1 (3.5- fold) and MeCP2 (2.5-fold) knock down clones. A combined participation of these three enzymes in the corepression of the methylated 5-LO promoter is indicated. Taken together, the data reveal that epigenetic mechanisms are strongly involved in the regulation of 5-LO transcription and might function as a crucial control mechanism of 5-LO expression.
Solid state NMR is a emerging method for the study of membrane proteins, which has received much interest in recent years. Limiting the study of many pharmacologically relevant targets, are the often long measuring times, required to obtain especially higher dimensional solid state NMR spectra of good quality. To address this problem, multiple methods where developed in this work, which can be categorized into two groups. The first set of methods aims at the quality of certain spectra, by implementing a spectral filter, which increases the fidelity of the measured data. The second set of methods, addresses the problem of long measuring times directly, by increasing the sensitivity per unit time, as could be shown, for example, on homo- and heteronuclear singlequantum-singlequantum correlation experiments. The gains in measuring time for the latter group of methods are typically in the order of 2-3, but some experiments allow multiple methods to be employed simultaneously, which can lead to a decrease in measuring time of a factor of up to 8. It is important to mention, that none of the methods introduced in this work require any equipment in addition to the conventional setup present in most sold state NMR laboratories and no changes or addition to the samples under study are required. Therefore the gains reported in this work come at no extra cost and require only minimal implementation effort on the side of the user.
In the production of integrated circuits (ICs), photolithography plays a key role in wafer structuring. The basic principle of photolithography is the selective processing of areas (etching, implantation, metallisation etc.) while the others are covered and therefore protected by the resist. After each process step the resist, now modified, has to be removed. In the history of semiconductor manufacturing this has been accomplished with a mixture of H2SO4 and H2O2, H2SO4 and O3 or a plasma etch. As the structure sizes decreased they reached a stage where they had to be exposed to light of shorter wavelengths for the photolithography, going from i-line (365 nm) to DUV (248 nm and 193 nm). This change in wavelength now requires new resists and therewith new stripping methods. Beside the changes in the resist the finer structures are also more sensitive to damages caused by the resist strip. Along with this the demand for cost reduction and environment-friendliness poses a big challenge for modern resist stripping. In this study ozone in deionised water (DI/O3) was the basic chemistry investigated as it is cost efficient in production and disposal as well as environment friendly. Furthermore it is a chemistry known to cause no damage to the wafers. DI/O3 has been successfully applied to strip i-line resists. The challenge now is to find ways and means to make DI/O3 strip even highly implanted DUV resists which currently can only be removed by a plasma etch. To achieve this a detailed understanding of the behaviour of ozone in DI water and the influence of factors both chemical and physical on the stripping efficiency at the different stages in the process is necessary. Along with this, methods which enable the elucidation of resist structures and the changes they undergo during the process of photolithography as well as during the ozone strip have to be developed. This will enable us to understand the mechanisms involved and hence, ideally, develop ozone-based stripping solutions customized for each resist and process step. For this purpose the ozone decomposition in DI water with and without additives was studied via UV-Vis spectroscopy. Radicals generated within the ozone decomposition were trapped and quantified, the resists were studied directly on the wafer with IR and Raman spectroscopy and stripped with DI/O3-mixtures and different setups to find optimum conditions for a complete and damage free resist strip. UV-Vis spectroscopy at 260 nm was used to study ozone decomposition and the factors, both chemical and physical, which influence it. These factors are pH, different additives at the same pH, temperature and mixing of the solution. For the radical determination trapping reactions with MeOH and DMSO both forming CH2O which is further converted to DDL as the detectable species were compared with a variation of the classical iodometric titration acting as an absolute method without the need of calibration. IR spectroscopy proved to be a suitable method for the structural characterisation of the resists and the tracking of the changes undergone during the various processing steps as well as the ozone based stripping. For the stripping with DI/O3 IR spectroscopy delivered well-defined spectra. These displayed significant peak changes which support the assumption of classical ozonolysis as the decomposition mechanism for the unimplanted resist. For the study of the resist crust originating from ion implantation IR was fundamentally unsuitable and was replaced by Raman spectroscopy and microscopy. Raman spectra showed the crust to be of a highly carbon containing structure. Regrettably, the peak assignable to the crust was too broad for the exact composition of the crust to be determined. The wavelength region of the peak corresponds to that of peaks of glassy carbon and highly ordered and conventional graphite. Such a broad peak suggests that the structure of the crust is not uniform but contains more than one carbon modification. As the purpose of all these studies is to enable or improve DI/O3 based resist stripping on unimplanted as well as high-dose implanted resists the removal efficiency of DI/O3 spiked with different additives that alter the pH was studied. For these unimplanted resists the maximum efficiency could be achieved at pH = 5 – 7. Lowering or increasing the pH beyond this range gave poor results. The stripping of highly implanted resists could be achieved only at harsh conditions with a high pH-level of 12 - 13 with a narrow process window showing no stripping at lower pHs and severe damages at higher levels. The principle application of DI/O3 stripping chemistry could be proved but the currently required process time unfortunatelly is too long for commercial application and needs further optimisation.
The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.
The transcription factor p63 is expressed as at least six different isoforms, of which two have been assigned critical biological roles within ectodermal development and skin stem cell biology on the one hand and supervision of the genetic stability of oocytes on the other hand. These two isoforms contain a C-terminal inhibitory domain that negatively regulates their transcriptional activity. This inhibitory domain contains two individual components: one that uses an internal binding mechanism to interact with and mask the transactivation domain and one that is based on sumoylation. We have carried out an extensive alanine scanning study to identify critical regions within the inhibitory domain. These experiments show that a stretch of ~13 amino acids is crucial for the binding function. Further, investigation of transcriptional activity and the intracellular level of mutants that cannot be sumoylated suggests that sumoylation reduces the concentration of p63. We therefore propose that the inhibitory function of the C-terminal domain is in part due to direct inhibition of the transcriptional activity of the protein and in part due to indirect inhibition by controlling the concentration of p63. Keywords: p63, transcriptional regulation, auto-inhibition, sumoylation
Misregulated receptor tyrosine kinases (RTKs), i.e. the epidermal growth factor receptor EGFR or the insulin-like growth factor receptor 1 (IGF-1R), can be involved in the development of cancer. Monoclonal antibodies specifically inhibit the RTKs in cancer therapy. The scope of this thesis is to investigate the molecular basis of the inhibition through the therapeutic antibodies matuzumab (EMD72000) against EGFR and EMD1159476 against IGF-1R. The 3D crystal structure of matuzumab in complex with the EGFR domain III shows an eptiope connected with a novel inhibition mechanism: a non-competitive, sterical inhibition of receptor acitivation. The anti-IGF-1R targeted monoclonal antibody EMD1159476 shows a reduced binding capacity to the receptor in the presence of ligand indicating a competitive inhibition mechanism. The epitope of EMD1159476 is within domain II of the receptor. The results of these molecular interaction studies are important for the clinical therapies with these monoclonal antibodies. The matuzumab-EGFR complex crystal structure shows that a simultaneous binding of matuzumab and cetuximab (Erbitux) is possible. The latter antibody is already in clinical use. A combination of several therapeutic antibodies in cancer treatment might show synergistic effects and benefits for the patients.
A solid-supported membrane (SSM) is an alkanethiol/lipid hybrid membrane with comparable lipid mobility, conductivity, and capacitance than a black lipid membrane (BLM). However, mechanical perturbations, which usually destroy a BLM, do not influence the life-time of a SSM, which is mechanically so stable that solutions may be rapidly exchanged at its surface. This key property has been utilized in this thesis to characterize electrophysiologically two bacterial secondary active transporters (MelB and LacY) as well as to investigate the specific interactions between ions and lipid membranes. These three different projects are summarized below: (1) The properties of lipid membranes, which represent the most important biological interface between intracellular and extracellular compartments, are essentially modulated by the ionic composition of the surrounding aqueous medium. To investigate specific interactions between ions and lipid membranes, solutions of different ionic composition were exchanged at the surface of a SSM through a flow system. This solution exchange resulted in charge translocations that were interpreted in terms of binding of the ions to the lipid headgroups at the SSM surface. We found that chaotropic anions and kosmotropic cations are attracted to the membrane independent of the membrane composition. In particular, the same behaviour was found for lipid headgroups bearing no charge like monoolein. This general trend is modulated by the electrostatic interaction of the ions with the lipid headgroup charge. Our experimental results are in agreement with recent molecular dynamic simulations of PC membranes. (2) Rapid solution exchange on a solid-supported membrane (SSM) is investigated using fluidic structures and a solid-supported membrane in a wall jet geometry. The flow was analyzed with a new technique based on specific ion interactions with the surface combined with an electrical measurement. The critical parameters affecting the time course of the solution exchange and the transfer function describing the time resolution of the SSM system were determined. The experimental data indicate that the solution transport follows a plug flow geometry while the rise of the surface concentration can be approximated by Hagen Poiseuille flow with ideal mixing at the surface of the SSM. Using an improved cuvette design a solution exchange as fast as 2 ms was achieved at the surface of a solid supported membrane. As an application of the technique the rate constant of a fast electrogenic reaction in the melibiose permease MelB, a bacterial (Escherichia coli) sugar transporter, is determined. For comparison, the kinetics of a conformational transition of the same transporter was measured using stopped-flow tryptophan fluorescence spectroscopy. The relaxation time constant obtained for the charge displacement agrees with that determined in the stopped-flow experiments. This supports the previous proposition that upon sugar binding MelB undergoes an electrogenic conformational transition with a rate constant of k ~ 250 s-1. (3) Electrogenic events due to activity of wild-type lactose permease from Escherichia coli (LacY) were investigated with proteoliposomes containing purified LacY adsorbed on a solid-supported membrane electrode. Downhill sugar/H+ symport into the proteoliposomes generates transient currents. Studies at different lipid to protein ratios and at different pH values, as well as inactivation by N-ethylmaleimide, show that the currents are due specifically to the activity of LacY. From analysis of the currents under different conditions and comparison with biochemical data, it is apparent that the predominant electrogenic event in downhill sugar/H+ symport is H+ release. In contrast, LacY mutants E325A and C154G, which bind ligand normally but are severely defective with respect to lactose/H+ symport, exhibit a minor electrogenic event upon addition of LacY-specific substrates, representing only 6% of the total charge displacement of the wild-type. This activity is due either to substrate binding per se or to a conformational transition following substrate binding. We propose that turnover of LacY involves at least two electrogenic reactions: (i) a minor reaction that occurs upon sugar binding and is due to a conformational transition in LacY; and (ii) a major reaction due to cytoplasmic release of H+ during downhill sugar/H+ symport, which is the limiting step for this mode of transport.
Specific functions of biological systems often require conformational transitions of macromolecules. Thus, being able to describe and predict conformational changes of biological macromolecules is not only important for understanding their impact on biological function, but will also have implications for the modelling of (macro)molecular complex formation and in structure-based drug design approaches. The “conformational selection model” provides the foundation for computational investigations of conformational fluctuations of the unbound protein state. These fluctuations may reveal conformational states adopted by the bound proteins. The aim of this work is to incorporate directional information in a geometry-based approach, in order to sample biologically relevant conformational space extensively. Interestingly, coarse-grained normal mode (CGNM) approaches, e.g., the elastic network model (ENM) and rigid cluster normal mode analysis (RCNMA), have emerged recently and provide directions of intrinsic motions in terms of harmonic modes (also called normal modes). In my previous work and in other studies it has been shown that conformational changes upon ligand binding occur along a few low-energy modes of unbound proteins and can be efficiently calculated by CGNM approaches. In order to explore the validity and the applicability of CGNM approaches, a large-scale comparison of essential dynamics (ED) modes from molecular dynamics (MD) simulations and normal modes from CGNM was performed over a dataset of 335 proteins. Despite high coarse-graining, low frequency normal modes from CGNM correlate very well with ED modes in terms of directions of motions (average maximal overlap is 0.65) and relative amplitudes of motions (average maximal overlap is 0.73). In order to exploit the potential of CGNM approaches, I have developed a three-step approach for efficient exploration of intrinsic motions of proteins. The first two steps are based on recent developments in rigidity and elastic network theory. Initially, static properties of the protein are determined by decomposing the protein into rigid clusters using the graph-theoretical approach FIRST at an all-atom representation of the protein. In a second step, dynamic properties of the molecule are revealed by the rotations-translations of blocks approach (RTB) using an elastic network model representation of the coarse-grained protein. In the final step, the recently introduced idea of constrained geometric simulations of diffusive motions in proteins is extended for efficient sampling of conformational space. Here, the low-energy (frequency) normal modes provided by the RCNMA approach are used to guide the backbone motions. The NMSim approach was validated on hen egg white lysozyme by comparing it to previously mentioned simulation methods in terms of residue fluctuations, conformational space explorations, essential dynamics, sampling of side-chain rotamers, and structural quality. Residue fluctuations in NMSim generated ensemble is found to be in good agreement with MD fluctuations with a correlation coefficient of around 0.79. A comparison of different geometry-based simulation approaches shows that FRODA is restricted in sampling the backbone conformational space. CONCOORD is restricted in sampling the side-chain conformational space. NMSim sufficiently samples both the backbone and the side-chain conformations taking experimental structures and conformations from the state of the art MD simulation as reference. The NMSim approach is also applied to a dataset of proteins where conformational changes have been observed experimentally, either in domain or functionally important loop regions. The NMSim simulations starting from the unbound structures are able to reach conformations similar to ligand bound conformations (RMSD < 2.4 Å) in 4 out of 5 cases of domain moving proteins. In these four cases, good correlation coefficients (R > 0.7) between the RMS fluctuations derived from NMSim generated structures and two experimental structures are observed. Furthermore, intrinsic fluctuations in NMSim simulation correlate with the region of loop conformational changes observed upon ligand binding in 2 out of 3 cases. The NMSim generated pathway of conformational change from the unbound structure to the ligand bound structure of adenylate kinase is validated by a comparison to experimental structures reflecting different states of the pathway as proposed by previous studies. Interestingly, the generated pathway confirms that the LID domain closure precedes the closing of the NMPbind domain, even if no target conformation is provided in NMSim. Hence, the results in this study show that, incorporating directional information in the geometry-based approach NMSim improves the sampling of biologically relevant conformational space and provides a computationally efficient alternative to state of the art MD simulations.
This thesis describes the structural characterization of interactions between biological relevant ribonucleic acid biomacromolecules (RNAs) and selected ligands to optimize the methodologies for the design of pharmacological lead compounds. To achieve this aim, not only the structures of the RNA, the ligand and their complexes need to be known, but also information about the inherent dynamics, especially of the target RNA, are necessary. To determine the structure and dynamics of these molecules and their complexes, liquid state nuclear magnetic resonance spectroscopy (NMR) is a suitable and powerful method. The necessity for these investigations arises from the lack of knowledge in RNA-ligand interactions, e.g. for the development of new medicinal drugs targeting crucial RNA sequences. In the first chapters of this thesis (Chapters II to IV), an introduction into RNA research is given with a focus on RNA structural features (Chapter II), into the interacting molecules, the biology of the specific RNA targets and the further development of their ligands (Chapter III) and into the NMR theory and methodologies used within this thesis (Chapter IV). Chapter II begins with a description of RNA characteristics and functions, placing the focus on the increasing attention that these biomacromolecules have attracted in recent years due to their diverse biological functionalities. This is followed by a detailed description of general structural features of RNA molecules. The biological functions of the RNAs investigated in this thesis (Human immunodeficiency virus PSI- and TAR-RNA and Coxsackievirus B3 Stemloop D in the 5’-cloverleaf element), together with their known structural characteristics are introduced in Chapter III. Furthermore, a description of the investigated ligands is given, focusing on the methods how their affinity and specificity were determined. The introduction is completed in Chapter IV, where the relevant NMR theory and methodologies are explained. First, kinetics and thermodynamics of ligand binding are summarized from an NMR point of view. Subsequently, a detailed description of the resonance assignment procedures for RNAs and peptidic ligands is given. This procedure mainly concentrates on the assignment of the proton resonances, which are essential for the later structure calculation from NMR restraints. The procedure for NMR structure calculation of RNA and its complexes follows with a short introduction into the programs ARIA and HADDOCK. The final part of this chapter explains the relaxation theory and the methodology to extract dynamic information from autocorrelated relaxation rates via the model-free formalism. In the Chapters V to VII of this thesis, the original publications are included and grouped into three topics. Chapter V comprehends the publications on the investigations of HIV PSI-RNA and its hexapeptidic ligand. These three publications[1-3] focus on the characterization of the ligand and its binding properties, its structure and the optimization of its composition aiming to improve its usage for further spectroscopic investigations.
The aim of the study was to investigate the role of the CX3C chemokine FKN in the role of platelet adhesion. The presence of the FKN receptor CX3CR1 in platelets is demonstrated and G-protein dependent activation of platelets with soluble FKN results in the increased adhesion of platelets to collagen and fibrinogen under flow 228 and adhesion of leucocytes to firmly attached platelets 231. Whether membrane-bound FKN is capable to promote the direct adhesion of platelets in flowing blood analogue to leucocytes was completely unknown. The adhesion mechanisms of FKN in mediating the adhesion of leucocytes under flow are well characterised and represent a novel unique mechanism of leucocyte capture and firm adhesion: FKN is responsible for immediate arrest of flowing CX3CR1 expressing leucocytes without the participation of additional adhesion receptors and ligands. This is in contrast to the classical leucocyte adhesion pathways, which are multistep processes involving leucocyte arrest, rolling and subsequent cell activation prior to firm arrest. In leucocytes, the FKN – CX3CR1 axis is sufficient to allow rapid arrest of leucocytes at low shear flow conditions 67, 101, 115, 122, 261. The set of data from this study demonstrates that immobilised FKN was capable to mediate the adhesion of platelets under low shear conditions, whereas there was no interaction in the absence of shear flow. In the presence of vWf in the adhesion matrix, FKN mediated the potent increased adhesion of platelets. This was in parts due to the activation of flowing platelets via CX3CR1 and the augmented translocation of platelets on FKN via the vWf receptor GPIbα. With respect to platelet activation, the function of endothelial FKN was comparable to leucocytes: in both cell types, the FKN dependent activation is mediated by its cognate receptor CX3CR1. This is in contrast to the adhesive capacity: in leucocytes, FKN dependent adhesion is mediated by CX3CR1, whereas in platelets, the adhesive capacity was mostly mediated by the vWf receptor GPIbα with only minor contribution from CX3CR1. In platelets, activation and adhesion by FKN were mediated by two distinct receptors, whereas in leucocytes, CX3CR1 is solely responsible for FKN dependent activation and adhesion. The presented results point out to a role of platelets in early stage of atherosclerosis. The in vivo expression of both, FKN and vWf is regulated by TNF-α, which is released in early stages of inflammation. The presence of vWf and FKN in the endothelial lining of blood vessels during these conditions is sufficient to initiate the capturing and translocation of platelets on the tunica interna. The rolling of platelets on the endothelium can induce endothelial damage and inflammation of the vessel, which might advance to the generation of clinically significant atherosclerotic plaques and fibrous atheroma.
P2X receptors represent the third superfamily of ligand gated ion channels with ATP as their natural ligand. Most of the mammalian P2X receptors are non-selective cation channels, which upon activation, mediate membrane depolarization and have physiological roles ranging from fast excitatory synaptic transmission, modulation of pain-sensation, LTP to apoptosis etc. In spite of them being an attractive drug target, their potential as a drug target is limited by the lack of basic understanding of the structure-function relationship of these receptors. In my thesis, I have investigated the behavior of homomeric P2X receptor subunits with the help of photolabeling and fluorescence techniques coupled to electrophysiological measurements using Xenopus laevis oocytes heterologous expression system. Concurrent photolabeling by BzATP and current recordings from the same set of receptors in real time has revealed that the gating process in homomeric P2X receptors is contributed individually by each subunit in an additive manner. Our study for the first time describes the agonist potency of Alexa-ATP (a fluorescent ATP analog) on P2X1 receptors. The use of Alexa-ATP in our experiments elucidated that receptor subunits are not independent but interacting with each other in a cooperative manner. The type of cooperativity, however, depended on the type and concentrations of allosteric/competing ligands. Based on our results, in my thesis we propose an allosteric model for ligand-receptor interactions in P2X receptors. When simulated, the model could replicate our experimental findings thus, further validating our model. Further, correlation between occupancy of P2X1 receptors (determined using binding curve for Alexa-ATP) with the steady-state desensitization suggests that binding of three agonist molecules per receptor are required to desensitize P2X1 receptors. We further extended the approach of fluorescence with electrophysiological measurement to assign the role for different domains in P2X1 receptors with the help of environmental sensitive, cysteine reactive fluorophore (TMRM). Cysteine rich domain-1 of P2X1 receptors (C117-C165) was found to be involved in structural rearrangements after agonist and antagonist binding. In contrast to the present understanding, that the binding of an antagonist cannot induce desensitization in P2X1 receptors and the receptors need to open first before undergoing desensitization, we propose based on our results that a competitive antagonist can also induce desensitization in P2X1 receptors by bypassing the open state. We have attempted to answer few intriguing questions in the field of P2X receptor research and we think that our answers provide many avenues to the basic understanding of functioning of P2X receptors.
Introduction: Immune paralysis with massive T-cell apoptosis is a central pathogenic event during sepsis and correlates with septic patient mortality. Previous observations implied a crucial role of peroxisome proliferator-activated receptor gamma (PPARγ) during T-cell apoptosis.
Methods: To elucidate mechanisms of PPARγ-induced T-cell depletion, we used an endotoxin model as well as the caecal ligation and puncture sepsis model to imitate septic conditions in wild-type versus conditional PPARγ knockout (KO) mice.
Results: PPARγ KO mice showed a marked survival advantage compared with control mice. Their T cells were substantially protected against sepsis-induced death and showed a significantly higher expression of the pro-survival factor IL-2. Since PPARγ is described to repress nuclear factor of activated T cells (NFAT) transactivation and concomitant IL-2 expression, we propose inhibition of NFAT as the underlying mechanism allowing T-cell apoptosis. Corroborating our hypothesis, we observed up-regulation of the pro-apoptotic protein BIM and downregulation of the anti-apoptotic protein Bcl-2 in control mice, which are downstream effector proteins of IL-2 receptor signaling. Application of a neutralizing anti-IL-2 antibody reversed the pro-survival effect of PPARγ-deficient T cells and confirmed IL-2-dependent apoptosis during sepsis.
Conclusion: Apparently antagonizing PPARγ in T cells might improve their survival during sepsis, which concomitantly enhances defence mechanisms and possibly provokes an increased survival of septic patients.
Na+/H+ antiporters are ubiquitous membrane proteins involved in ion homeostasis and pH sensing. The amino acid sequence of one such antiporter, MjNhaP1, from Methanococcus jannaschii, shows a significant homology to eukaryotic sodium proton exchangers like NHE1 from Homo sapiens and SOS1 of Arabidopsis thaliana than to the well-characterized Escherichia coli NhaA or NhaB. MjNhaP1 shows activity at acidic pH unlike NhaA, which is active at basic pH. 13 transmembrane helices have been predicted to be present in NhaP1. A projection map, calculated by Cryo-EM of 2D crystals of MjNhaP1 grown at pH 4, showed it to be a dimer containing elongated densities in the centre of the dimer and a cluster of density peaks on either side of the dimer core (Vinothkumar et al., 2005). Incubation of 2D crystals at pH 8 on the EM grid resulted in well-defined conformational changes, clearly evident in a difference map as a major change in density distribution within the helix bundle (Vinothkumar et al., 2005). The aim of this dissertation is to understand the working mechanism of MjNhaP1 by determining its three-dimensional structure. The aim was initially approached by structure determination by X-ray crystallography. The limitation for this method was the low expression yield, which was 0.5–0.7mg/ml (Vinothkumar et al., 2005). After various optimization trials, the expression yield of the recombinant protein could be elevated to 2-2.5mg of pure protein per litre of culture by the method of autoinduction (Studier et al., 2005). To obtain well diffracting 3D crystals, purification conditions (Vinothkumar et al., 2005) were modified. 3D crystals were obtained under various conditions, which has so far not diffracted X-Ray beyond 8Å. Parallely, optimization of parameters (Vinothkumar et al., 2005) for 2D crystals formation was carried out. A combination of 1% DDM used for lipid solubilization, and 1% OG in the buffer of the purified protein produced 1-2 μm wide tubular 2D crystals of NhaP1. This batch of crystal proved to be the optimal for data collection at higher tilt angle with the electron microscope. A 3D map showed p22121 symmetry and revealed a tight dimer with an oval shape. The region in the central part of the dimer is composed of several tilted helices forming an interface between both monomers. On either side of the dimer interface, a group of six tightly packed helices form a bundle. This bundle contains three straight helices in the centre of the monomer and three helices in the periphery. Comparison of the structures of E.coli NhaA and M. jannaschii NhaP1 show substantial differences in length and slope of corresponding helices between both antiporters. A 3D model of NhaP1 based on the 3D map revealed 13 helices, which has been named as A-M to distinguish it from the NhaA helices. Overlaying the X-ray structure onto the 3D map revealed that the disrupted helices IV and XI of NhaA superimpose two central helices at similar position in the 3D map of NhaP1. The disrupted helices IV and XI in the X-ray structure of NhaA have been proposed as the putative ion-binding and translocation site (Hunte C et al, 2005; Arkin IT et al, 2007; Screpanti & Hunte (2007). This motif appears to be present also in NhaP1, as suggested by the close fit of NhaA helices IV and XI on the putative helices E and L of the NhaP1 model. These two putative helices E and L in NhaP1 contain the highly conserved TDP and GPRVVP motif, which are crucial for antiporter activity (Hellmer et al., 2002, Hellmer et al., 2003). In the overlay, helix V of NhaA containing the two essential, conserved aspartates D163 and D164 fits the density of the putative helix F of NhaP1, which contains the conserved motif FNDP. The homologous D161 in the FNDP motif of NhaP1 is essential for transport activity as show by mutagenesis (Hellmer at al., 2003). Significant differences are visible in the region of the dimer interface of the 3D map of NhaP1 occupied by helices VI, VII, and VIII in NhaA. This region shows an extra helical density (A) in the 3D map of NhaP1. By alignment of MjNhaP1 sequence with the amino acid sequences of several Na+/H+ exchangers, it was evident that the additional helix (A) is located in the N terminus of NhaP1. In our sequence alignment, a putative hydrophobic segment corresponding to this additional helix A is present in other archaeal and eukaryotic antiporters but not in any of the bacterial ones. The N-terminus of the human Na+/H+ exchanger NHE1 has been predicted to contain a highly hydrophobic signal peptide. This indicates the probability of the N-terminal helix A of NhaP1 to be an uncleaved signal peptide. Besides being a signal sequence targeting NhaP1 to the membrane, the map suggests that this helix might be involved in the formation of dimer contacts between both monomers. A gene duplication event is evident in the 3D map of NhaP1, as not only the helices D, E, F and K, L, M are related by an inverted repeat but also the helices B, C and I, J are related. We present here the three-dimensional architecture of a Na+/H+ antiporter from archaea. The presence of the 13th helix suggests the location of the N-terminus to be located in the cytosol and the C-terminus in the periplasm. This would orient NhaP1 in an inverted manner in the membrane in comparison to NhaA. Further structural information at higher resolution and biochemical and biophysical investigations are required to confirm the topology.
The transcription factor p63 is part of the p53 protein family, which consists of three members, p53, p63 and p73. P63 shares structural similarity with all family members, but is associated to different biological functions than p53 or p73. While p53 is mainly linked to tumor suppression and p73 is connected with neuronal development, p63 has been connected to critical biological roles within ectodermal development and skin stem cell biology as well as supervision of the genetic stability of oocytes. Due to its gene structure p63 is expressed as at least six different isoforms, three of them containing a N-terminal transactivation domain. The isoforms that are of biological relevance both have a C-terminal inhibitory domain that negatively regulates the transcriptional activity. This inhibitory domain is supposed to contain two individual components of which one is internally binding and masking the transactivation domain while the other one can be sumoylated. To further investigate this domain a mutational analysis with the help of transactivation assays in SAOS2 cells was carried out to identify the critical amino acids within the inhibitory domain and the impact on transcriptional activity of TAp63alpha, the p63-isoform which is essential for the integrity of the female germline. The results of these experiments show that a stretch of approximately 13 amino acids seems to be important for the regulation of transcriptional activity in TAp63alpha, due to the increased transcriptional activity occurring in this region after mutation. Additional experiments showed that this mechanism is distinct from sumoylation, which seems to have only implications for the intracellular level of TAp63alpha. As a conclusion, the C-terminus of the Tap63alpha is essential for two different mechanisms, which control the transcriptional activity of the protein. Both regulatory elements are independent from each other and can now be restricted to certain amino acids. Activation of the wild type protein might take place in the identified region via post-translational modification. Furthermore an inhibition assay was carried out to test if the same region might have implications on the second biological relevant isoform deltaNp63alpha. The results show that the same amino acids which show an impact on transcriptional activity in Tap63alpha lead to a significant change in functional behaviour of deltaNp63alpha. There is a possibility that both proteins are regulated with opposite effects via the same mechanisms, based at the C-terminus of the p63alpha-isoforms. In both cases a modification of these residues could lead to a more opened conformation of the protein with consequences on promoter binding, which can be even important for deltaNp63alpha with respect to promoter squelching. Both alpha-isoforms seem to be regulated via the C-terminus and to elucidate if that is also the case for TAp63gamma a deletion analysis was carried out. The results show that there are also amino acids within the C-terminus of TAp63gamma, which have implications on the transcriptional activity of the protein. Therefore the C-terminus seems to play a major role for regulation of diverse p63 isoforms.
Based on the commonly used and well-established state-of-the-art DNA sequencing method, i. e. Sanger sequencing, the major target of future research is to develop a fast, cost-effective and gelelectrophoresis-free sequencing method. The aim of the new sequencing technologies is to detect DNA mutations faster and more accurate in order to develop individual therapies for patients (personalized medicine). For this purpose, a lot of novel sequencing techniques like pyrosequencing, mass-spectrometry-assisted sequencing, sequencing by hybridization etc. have been put into practice and already led to commercialized sequencers. The sequencing technology we were mostly interested in is the so-called sequencing-by-synthesis method (SBS). This PhD thesis covers the synthesis of modified nucleosides – the so-called reversible terminators – and their evaluation as reversible terminators. These 3′-modified and dye-labeled nucleotides are incorporated by the polymerase into the DNA-template, then the DNA-synthesis is stopped. After detection of the fluorescent signal, the reversible terminator has to be cleavable in a way (i. e. the polymerase-blocking modification) that the DNA-synthesis can continue. As a result of the polymerase-acceptance tests that have been carried out with the two triphosphates cyanoethoxymethyl(CEM)-dTTP and cyanoethyl(CE)-dTTP as substrates it became clear that the latter one was better incorporated than the first one. Based on this knowledge all four key compounds for the whole reversible terminators possessing the cyanoethyl (CE) group where synthesized within this PhD thesis. Additionally to the synthesis of the modified key compounds, the cleavability of the cyanoethyl function had to be evaluated which is an essential requirement of a reversible terminator for SBS. For addressing this issue, three different CE- and CEM modified monophosphates were created. For each of these three monophosphates an individual synthetic strategy has been developed within this PhD work, each of these strategies and subsequent phosphorylation led to the desired modification. These previously unknown model compounds mimicking the solubility of short oligonucleotides were employed the for qualitative cleavage experiments after their purification and spectroscopical characterization. With these three monophosphates suitable cleavage conditions for a quantitative removal of the CE and the CEM group were examined. In case of the CE function we selectively improved the cleavage conditions while varying the solvent, the reaction temperature as well as the amount of cleaving agent used, in order to make the conditions applicable for an SBS experiment. Due to the fact that the CE function was the most important modification for our SBS experiment, we could even optimize the cleavage efficiency by employing co-solvents like DMSO or DMF. An additional cleavage experiment was carried out by using a short CE-modified oligomer which led to further results that were comparable to the ones obtained from the cleavage experiments of the monomers. One big difference is the required amount of TBAF as cleaving agent for the quantitative removal of the CE-modification from the oligomer. In this case, 7500 equivalents of TBAF are needed for complete CE cleavage at 45 °C compared to the amount of 40 to 80 equivalents TBAF for the monomer (monophosphate). As a conclusion of this result we assume that the amount of cleaving agent and the solubility of the oligomer plays an important role in the CE cleavage efficiency. This assumption was already supported by Saneyoshi et al. who demonstrated for CE-modified RNA oligonucleotides that the CE-cleavage rate is strongly lowered with the increasing of the oligomer length. Thus we could demonstrate that the CE function is quantitatively removable from an oligomer without destroying it. With these results in hands we could prove that the CEM and the CE group are quantitatively cleavable and therefore applicable as blocking groups for reversible terminators. The conditions for the CE cleavage are used for the ArraySBS-“proof-of-principle” which is currently under investigation.
X-ray structure of the Na+-coupled Glycine-Betaine symporter BetP from Corynebacterium glutamicum
(2009)
Cellular membranes are important sites of interaction between cells and their environment. Among the multitude of macromolecular complexes embedded in these membranes, transporters play a particularly important role. These integral membrane proteins perform a number of vital functions that enable cell adaptation to changing environmental conditions. Osmotic stress is a major external stimulus for cells. Bacteria are frequently exposed to either hyperosmotic or hypoosmotic stress. Typical conditions for soil bacteria, such as Corynebacterium glutamicum, vary between dryness and sudden rainfall. Physical stimuli caused by osmotic stress have to be sensed and used to activate appropriate response mechanisms. Hypoosmotic stress causes immediate and uncontrolled influx of water. Cells counteract by instantly opening mechanosensitive channels, which act as emergency valves leading to fast efflux of small solutes out of the cell, therebydiminishing the osmotic gradient across the cell membrane. Hyperosmotic stress, on the other hand, results in water efflux. This is counterbalanced by an accumulation of small, osmotically active solutes in the cytoplasm, the so-called compatible solutes. They comprise a large variety of substances, including amino acids (proline), amino acid derivatives (betaine, ectoine), oligosaccharides (trehalose), and heterosides (glucosylglycerol). Osmoregulated transporters sense intracellular osmotic pressure and respond to hyperosmotic stress by facilitating the inward translocation of compatible solutes across the cell membrane, to restore normal hydration levels. This work presents the first X-ray structure of a member of the Betaine-Choline-Carnitine-Transporter (BCCT) family, BetP. This Na+-coupled symporter from Corynebacterium glutamicum is a highly effective osmoregulated and specific uptake system for glycine-betaine. X-ray structure determination was achieved using single wavelength anomalous dispersion (SAD) of selenium atoms. Selenium was incorporated into the protein during its expression in methione auxotrophic E. coli cells, grown in media supplemented with selenomethionine. SAD data with anomalous signal up to 5 Å led to the detection of 39 selenium sites, which were used to calculate the initial electron density map of the protein. Medium resolution and high data anisotropy made the structure determination of BetP a challenging task. A specific strategy for data anisotropy correction and a combination of various crystallographic programs were necessary to obtain an interpretable electron density map suitable for model building. The crystal structure of BetP shows a trimer with glycine-betaine bound in a three-fold cation-pi interaction built by conserved tryptophan residues. The bound substrate is occluded from both sides of the membrane and aromatic side chains line its transport pathway. Very interestingly, the structure reveals that the alpha-helical C-terminal domain, for which a chemo- and osmosensory function was elucidated by biochemical methods, interacts with cytoplasmic loops of an adjacent monomer. These unexpected monomer-monomer interactions are thought to be crucial for the activation mechanism of BetP, and a new atomic model combing biochemical results with the crystal structure is proposed. BetP is shown to have the same overall fold as three unrelated Na+-coupled symporters. While these were crystallised in either the outward- or inward-facing conformation, BetP reveals a unique intermediate state, opening new perspectives on the alternating access mechanism of transport.
Structural analysis of the enzyme N-formylmethanofuran:tetrahydromethanopterin formyltransferase
(2008)
Archaea represent a third domain of life and some archaea exhibit a high degree of tolerance to extreme environmental conditions. Several members are methanogens and present in many anaerobic environments. Most methanogens are able to maintain growth simply on H2 and CO2 via the enzymatically catalyzed reaction 4H2 + CO2 > CH4 + 2 H2O. The archaeon Methanopyrus kandleri grows optimally at temperatures of 84°C to 110°C, pH values of 5.5 to 7.0 and NaCl concentrations 0.2% to 4%. The enzyme N-formylmethanofuran tetrahydromethanopterin formyltransferase (MkFTR) catalyzes the transfer of a formyl group from the cofactor N-formylmethanofuran (FMF) to the cofactor tetrahydromethanopterin (H4MPT), the second step of the above reaction. X-ray crystallographic analysis yielded insights into the structure and function of MkFTR, (1) the MkFTR monomer exhibits a pseudo-two fold structure suggestive of an evolutionary gene duplication. (2) The structure is a D2 homo-tetramer with prominent cleft-like surface features. Analysis of the interface contacts showed that the tetramer is best described as a dimer of dimers. The clefts were associated with the monomer:monomer interface and were weakly occupied by extra electron density which might be attributed to the H4MPT analog folate. (3) This suggested that the clefts are active sites and their association with oligomer interfaces suggested a basis for the dependence of activity on oligomerization. (4) The thermal stability of MkFTR most likely arises from the greater number of H- and ionic-bonds within the monomer and between monomers with respect to mesophilic protein structures. (5) The structure showed a large number of surface exposed negatively charged, glutamate and aspartate residues. These residues explain the salt dependent oligomerization, as only at high enough salt concentration is the electrostatic charge compensated by cation binding and neutralized allowing oligomerization. (6) These residues also improve the solubility of MkFTR at high salt concentration by increased charge repulsion. (7) Comparison of MkFTR structures from low and hight salt conditions showed that surface glutamate residues bind slightly more water molecules at high salt conditions further contributing to MkFTR solubility at high salt concentration.